Variant 5-103136856-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001276277.3(PPIP5K2):c.401+34A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 1,477,420 control chromosomes in the GnomAD database, including 1,081 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 528 hom., cov: 32)

Exomes 𝑓: 0.017 ( 553 hom. )

Consequence

PPIP5K2
NM_001276277.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.07

Variant links:

Genes affected

PPIP5K2 (HGNC:29035): (diphosphoinositol pentakisphosphate kinase 2) This gene encodes a member of the histidine acid phosphatase family of proteins. Despite containing a histidine acid phosphatase domain, the encoded protein functions as an inositol pyrophosphate kinase, and is thought to lack phosphatase activity. This kinase activity is the mechanism by which the encoded protein synthesizes high-energy inositol pyrophosphates, which act as signaling molecules that regulate cellular homeostasis and other processes. This gene may be associated with autism spectrum disorder in human patients. [provided by RefSeq, Sep 2016]

PPIP5K2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 5-103136856-A-G is Benign according to our data. Variant chr5-103136856-A-G is described in ClinVar as [Benign]. Clinvar id is 1261411.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPIP5K2	NM_001276277.3 linkuse as main transcript	c.401+34A>G		intron_variant		ENST00000358359.8	NP_001263206.1	O43314-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIP5K2	ENST00000358359.8 linkuse as main transcript	c.401+34A>G		intron_variant		1	NM_001276277.3	ENSP00000351126.3		O43314-1

Frequencies

GnomAD3 genomes

AF:

0.0520

AC:

7911

AN:

152184

Hom.:

526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0161

Gnomad ASJ

AF:

0.00577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.0397

GnomAD3 exomes

AF:

0.0195

AC:

4883

AN:

250774

Hom.:

245

AF XY:

0.0163

AC XY:

2206

AN XY:

135634

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.0106

Gnomad ASJ exome

AF:

0.00885

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00111

Gnomad FIN exome

AF:

0.00286

Gnomad NFE exome

AF:

0.0136

Gnomad OTH exome

AF:

0.0160

GnomAD4 exome

AF:

0.0166

AC:

22028

AN:

1325118

Hom.:

553

Cov.:

AF XY:

0.0155

AC XY:

10324

AN XY:

666722

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.0117

Gnomad4 ASJ exome

AF:

0.00743

Gnomad4 EAS exome

AF:

0.0000257

Gnomad4 SAS exome

AF:

0.00120

Gnomad4 FIN exome

AF:

0.00351

Gnomad4 NFE exome

AF:

0.0150

Gnomad4 OTH exome

AF:

0.0192

GnomAD4 genome

AF:

0.0521

AC:

7936

AN:

152302

Hom.:

528

Cov.:

AF XY:

0.0495

AC XY:

3684

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.0161

Gnomad4 ASJ

AF:

0.00577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.0132

Gnomad4 OTH

AF:

0.0393

Alfa

AF:

0.0288

Hom.:

Bravo

AF:

0.0583

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.91

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over